Reproducible Research Final Project
Covid-19 Automated Report
Didem Paloglu, 425160
Huseyin Can Minareci, 417121
1. INTRODUCTION
1.1. Aim of the Project
In this project, it is aimed to visualize the main insights about Covid-19 pandemic. Starting from ‘2020-01-01’ , pandemic data from all countries is recorded in the data set until ‘2021-05-05’. The data set is very useful and gives wide information about status of countries in pandemic period. There are information about cases, deaths, reproduction rates, intensive care unit (icu) patients, tests, positiveness rates, vaccinations etc. Moreover, there are also additional information giving basic demographic statistics and also health statistics about countries such as smoking status by gender, life expectancy, population and its distribution over 65+ and 70+ aged people.
The main objective is providing an automated report so that any one who wonder the situation about a country or in time period could select desired values and create the automatic report for that country/time line. The default country is selected as United States and the time period is selected to cover all records of the data set.
1.2. Information About Data Set
The dataset is extracted from Our World in Data and it can be downloaded from GitHub Covid-19 Repository. It contains 59 columns and 86,118 rows giving information about each region and country in the world. To give the main structure, the head of data set is provided below:
| iso_code | continent | location | date | total_cases | new_cases | new_cases_smoothed | total_deaths | new_deaths | new_deaths_smoothed | total_cases_per_million | new_cases_per_million | new_cases_smoothed_per_million | total_deaths_per_million | new_deaths_per_million | new_deaths_smoothed_per_million | reproduction_rate | icu_patients | icu_patients_per_million | hosp_patients | hosp_patients_per_million | weekly_icu_admissions | weekly_icu_admissions_per_million | weekly_hosp_admissions | weekly_hosp_admissions_per_million | new_tests | total_tests | total_tests_per_thousand | new_tests_per_thousand | new_tests_smoothed | new_tests_smoothed_per_thousand | positive_rate | tests_per_case | tests_units | total_vaccinations | people_vaccinated | people_fully_vaccinated | new_vaccinations | new_vaccinations_smoothed | total_vaccinations_per_hundred | people_vaccinated_per_hundred | people_fully_vaccinated_per_hundred | new_vaccinations_smoothed_per_million | stringency_index | population | population_density | median_age | aged_65_older | aged_70_older | gdp_per_capita | extreme_poverty | cardiovasc_death_rate | diabetes_prevalence | female_smokers | male_smokers | handwashing_facilities | hospital_beds_per_thousand | life_expectancy | human_development_index | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | AFG | Asia | Afghanistan | 2020-02-24 | 1 | 1 | NA | NA | NA | NA | 0.03 | 0.03 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 8.33 | 38928341 | 54.42 | 18.6 | 2.58 | 1.34 | 1803.99 | NA | 597.03 | 9.59 | NA | NA | 37.75 | 0.5 | 64.83 | 0.51 | |
| 2 | AFG | Asia | Afghanistan | 2020-02-25 | 1 | 0 | NA | NA | NA | NA | 0.03 | 0.00 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 8.33 | 38928341 | 54.42 | 18.6 | 2.58 | 1.34 | 1803.99 | NA | 597.03 | 9.59 | NA | NA | 37.75 | 0.5 | 64.83 | 0.51 | |
| 3 | AFG | Asia | Afghanistan | 2020-02-26 | 1 | 0 | NA | NA | NA | NA | 0.03 | 0.00 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 8.33 | 38928341 | 54.42 | 18.6 | 2.58 | 1.34 | 1803.99 | NA | 597.03 | 9.59 | NA | NA | 37.75 | 0.5 | 64.83 | 0.51 | |
| 4 | AFG | Asia | Afghanistan | 2020-02-27 | 1 | 0 | NA | NA | NA | NA | 0.03 | 0.00 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 8.33 | 38928341 | 54.42 | 18.6 | 2.58 | 1.34 | 1803.99 | NA | 597.03 | 9.59 | NA | NA | 37.75 | 0.5 | 64.83 | 0.51 | |
| 5 | AFG | Asia | Afghanistan | 2020-02-28 | 1 | 0 | NA | NA | NA | NA | 0.03 | 0.00 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 8.33 | 38928341 | 54.42 | 18.6 | 2.58 | 1.34 | 1803.99 | NA | 597.03 | 9.59 | NA | NA | 37.75 | 0.5 | 64.83 | 0.51 |
Note 1: The default country for the report is chosen as United States. If the user of the report does not specify any country, the report will be created for United States.
Note 2: The default time period for the report is chosen to cover all time range (between 2020-01-01 and 2021-05-05). If the user of the report does not specify any time period, the report will be created for all time period.
1.3. General Situation of Covid-19 Pandemic in the World
Before starting detailed analysis, it is beneficial to provide distribution and density of total Covid cases for all countries to give the general idea/information about what’s happening in the world. In below map, total cases (from first reported case to last reported case) in all avaliable countries between 2020-01-01 and 2021-05-05 is provided. The wider bubbles indicates the higher number of cases in countries.
2. DETAILED ANALYSIS ABOUT COVID-19
In this section, several analysis about Covid-19 pandemic is provided. All analysis are reported for United Kingdom in the time interval 2020-01-01 and 2021-05-05. It should be noted that one can produce different report results for other countries and time interval by changing the country and dates in the “Knit with Parameters” option.
Before jumping detailed visual analysis, the key highlights about Covid-19 are provided. This highlights give the general characteristics of Covid-19 pandemic in United Kingdom .General characteristics of COVID-19 in United Kingdom
Between 2020-01-01 and 2021-05-05, the number of total cases has been reach to 4441644 in United Kingdom. The maximum number of daily cases in this period has been reached to 68192, which is reported on 2021-04-28 and average daily case is 9635. In this period, 127830 people have died and maximum number of death is recorded as 1826 on 2021-01-20 and average daily death is 300. Reproduction rate is 1.09, which is below from world average (world average=1.16). It means that, on average, every 10 people with Covid will infect 11 other people.
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After giving general characteristics of the pandemic in the selected time period, the detailed analysis is helpful to see the pandemic trend deeply. The following sections shows the important analysis about the country.
2.1. Total Cases and Daily Cases
Explanation for the line graph will be here.
2.2. Daily Cases and Deaths
2.3. Daily Tests and Positive Rates
2.4. COVID-19 Hospitalizations
2.5. COVID-19 Vaccinations
General characteristics of COVID-19 Vaccination in United Kingdom
United Kingdom, uses Moderna, Oxford/AstraZeneca, Pfizer/BioNTech vaccines in order to fight with COVID-19.
Source: Government of the United Kingdom (https://coronavirus.data.gov.uk/details/healthcare).
Between 2020-01-01 and 2021-05-05, the number of total vaccination has been reach to 50682567 in United Kingdom. While 34795074 amount of people got only 1st dose of vaccination, 15887493 people got both doses and got fully vaccinated. The maximum number of vaccination per day in this period has been reached to 844285, which is reported on 2021-04-13 and average daily vaccination is 421093.
1st dose vaccination rate is 51 %, which is above from world average (world average= 14 %). And fully vaccinated rate is 23 %, which is above from world average (world average= 6 %).2.5.1. First Dose and Fully Vaccinated
In the following plot vaccinations in United Kingdom between 2020-01-01 and 2021-05-05 can be seen.
First day they started to vaccinate people in the United Kingdom was 2021-01-11. From that time until 2021-05-05 in total 34795074 person got at least 1 dose of vaccination while 15887493 people got fully vaccinated against covid. Maximum difference between at least 1st dose and fully vaccinated is 26833891 and it is 39.5 % of population which was seen on 2021-03-29. From other hand minimum difference is 2019481 and it is 3 % of population which happened on 2021-01-11. If it comes to average difference at least first dose and fully vaccination is 17765913 and it is 26.2 % of population which was around 2021-02-23.
2.5.2. COVID-19 Daily Vaccinations and Trend
In the following plot daily new vaccinations and trend in United Kingdom between 1st Day and 2021-05-05 can be seen.
If it comes to daily vaccination in the United Kingdom as we can see from the trend, it increases until 2021-04-02 and then decreases. Maximum new vaccination per day is 844285 and it is 1.2 % of population which was seen on 2021-03-20. From other hand minimum new vaccination is 95763 and it is 9576300 % of population which happened on 2021-04-04. If it comes to average daily new vaccinations is 421093 and it is 0.6 % of population which was around 2021-03-21.